R/Add_custom_vcfs.R

In RaikOtto/Younikorn: Identification of cancer cell lines based on their weighted mutational/ variational fingerprint

#' add_custom_vcf_to_database
#
#' This function adds the variants of parsed custom CCLs to a monet DB instance
#'  
#' @param vcf_input_files a character vector containing the input vcf files.
#'  This may be one or many vcf files.
#' @param ref_gen a character string specifying the reference genome version.
#'  All training sets are associated with a reference genome version.
#'  Default is \code{"GRCH37"}. 
#' @param library_name a character string giving the name of the library to add the
#'  cancer cell lines to. Default is \code{"CUSTOM"}. 
#'  Library name will be automatically added as a suffix to the identifier.
#' @param n_threads an integer specifying the number of threads to be used.
#' @param test_mode Is this a test? Just for internal use
#' @return Message wheather the adding was successful
#' @import GenomicRanges foreach
#' @usage 
#' add_custom_vcf_to_database(
#'     vcf_input_files,
#'     ref_gen = "GRCH37",
#'     library_name = "CUSTOM",
#'     n_threads = 1,
#'     test_mode = FALSE
#' )
#' @examples
#' HT29_vcf_file = system.file("extdata/HT29_TEST.vcf", package = "Uniquorn");
#' add_custom_vcf_to_database(
#'     vcf_input_files = HT29_vcf_file,
#'     library_name = "CELLMINER",
#'     ref_gen = "GRCH37",
#'     n_threads = 1,
#'     test_mode = TRUE
#' )
#' 
#' @export
add_custom_vcf_to_database = function(
    vcf_input_files,
    ref_gen = "GRCH37",
    library_name = "CUSTOM",
    n_threads = 1,
    test_mode = FALSE)
{
    
    #ccl_list = read_ccl_list(ref_gen = ref_gen, library_name = library_name)
    
    if (n_threads > 1){
        
        doParallel::registerDoParallel(n_threads)
        
        foreach::foreach(
            vcf_input_file = vcf_input_files
        ) %dopar% {
            g_query = parse_vcf_file(
                vcf_input_file,
                ref_gen = ref_gen,
                library_name = library_name
            )
            
            parse_vcf_query_into_db(
                g_query,
                ref_gen = ref_gen,
                test_mode = test_mode,
                library_name = library_name
            )
        }
        
        doParallel::stopImplicitCluster()
        
    } else {
        
        for (vcf_input_file in vcf_input_files){
            
            g_query = parse_vcf_file(
                vcf_input_file,
                ref_gen = ref_gen,
                library_name = library_name
            )
            
            parse_vcf_query_into_db(
                g_query,
                ref_gen = ref_gen,
                test_mode = test_mode,
                library_name = library_name
            )
        }
    }
    message("Finished")
}

#' parse_vcf_query_into_db
#
#' This function adds the variants of parsed custom CCLs to a monet DB instance
#'  
#' @param g_query a GenomicRanges object
#' @param ref_gen a character string specifying the reference genome version.
#'  All training sets are associated with a reference genome version.
#'  Default is \code{"GRCH37"}. 
#' @param library_name a character string giving the name of the library to add
#'  the cancer cell lines to. Default is \code{"CUSTOM"}. 
#'  Library name will be automatically added as a suffix to the identifier.
#' @param test_mode Is this a test? Just for internal use
#' @return Message wheather the adding was successful
#' @import GenomicRanges stringr
#' @importFrom IRanges findOverlaps
parse_vcf_query_into_db = function(
    g_query,
    ref_gen = "GRCH37",
    library_name,
    test_mode = FALSE
){
    
    cl_id = mcols( g_query )$Member_CCLs[1]
    cl_id = str_replace( cl_id, pattern = paste0("_", library_name), "")
    
    cl_data =  show_contained_ccls(verbose = FALSE)
    if (cl_id %in% cl_data$CCL[ cl_data$Library == library_name  ] ){
        stop("CCL ", cl_id, " already contained in DB ", library_name,
            ". Remove first or change name")
    }
    
    message("Sample: ", cl_id,", Library: ", library_name)
    
    g_mat = read_mutation_grange_objects(
        library_name = library_name,
        ref_gen = ref_gen,
        mutational_weight_inclusion_threshold = 0,
        test_mode = test_mode
    )
    
    if ( "Member_CCLs" %in% names(mcols(g_mat)) ){
        
        g_mat_new = unique(c(
            GenomicRanges::GRanges(g_mat),
            GenomicRanges::GRanges(g_query)
        ))
        fo_g_mat = findOverlaps(
            query = g_mat,
            subject = g_mat_new,
            select = "arbitrary",
            type = "equal"
        )
        
    } else {
        
        g_mat_new = unique(GenomicRanges::GRanges(g_query))
        fo_g_mat = GenomicRanges::GRangesList()
    }
    GenomicRanges::mcols(g_mat_new)$Member_CCLs = 
        rep("", length(g_mat_new))
    
    fo_query = findOverlaps(
        query = g_query,
        subject = g_mat_new,
        select = "arbitrary",
        type = "equal"
    )
    
    old_members = as.character( 
        sapply(as.character(elementMetadata(g_query)$Member_CCLs), 
            function(vec){
                ccl_ids = as.character(unlist(str_split(vec, pattern = ",")))
                ccl_ids = unique(ccl_ids)
                ccl_ids = paste(ccl_ids, collapse = ",", sep ="")
                return(ccl_ids)
            }
        )
    )
    
    mcols( g_mat_new )$Member_CCLs[fo_query] = old_members
    
    if ( "Member_CCLs" %in% names(mcols(g_mat)) )
        
        GenomicRanges::mcols( g_mat_new )$Member_CCLs[fo_g_mat]   =
            paste( 
                mcols( g_mat_new )$Member_CCLs[fo_g_mat],
                elementMetadata(g_mat)$Member_CCLs, sep = ","
            )
    
    GenomicRanges::mcols( g_mat_new )$Member_CCLs = stringr::str_replace( 
        GenomicRanges::mcols( g_mat_new )$Member_CCLs,
        pattern = "^,",""
    )
    g_mat = g_mat_new
    
    if(test_mode == FALSE){
        write_w0_and_split_w0_into_lower_weights(
            g_mat = g_mat,
            ref_gen = ref_gen,
            library_name = library_name
        )
    }
    
    message("Finished parsing ", cl_id, ", library: ", library_name)
}